Research workbench
Yeast DNA polymerase eta inserting dctp opposite an 8OXOG lesion
Analyse Yeast DNA polymerase eta inserting dctp opposite an 8OXOG lesion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OHA
- Type
- protein + DNA
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'…
- EC
- 2.7.7.7
- UniProt
- Q04049
- Ligands
- DCP, MG, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 516 | 42% helix, 19% strand | Q04049 |
| P | 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3' | dna | 11 | — | — |
| T | 5'-D(P*TP*(8OG)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3' | dna | 13 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, P
- SO4 · Sulfate ion · ion · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.82 | 0.84 | 87 | DCP, MG |
| 2 | 521 | 0.68 | 0.79 | 34 | SO4 |
| 3 | 52 | 0.39 | 0.81 | 17 | empty |
| 4 | 60 | 0.30 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 690 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 525 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 507 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q04049
- Elsewhere: RCSB PDB 3OHA · PDBe 3OHA · UniProt Q04049
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